Explore Workflows

View already parsed workflows here or click here to add your own

Graph Name Retrieved From View
workflow graph RNASelector as a CWL workflow

https://doi.org/10.1007/s12275-011-1213-z

 https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: workflows/rna-selector.cwl

Branch/Commit ID: 583307878ab83c5845c897f03db920ae8e1929e2
workflow graph RNA-Seq pipeline paired-end strand specific

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

 https://github.com/datirium/workflows.git

Path: workflows/rnaseq-pe-dutp.cwl

Branch/Commit ID: 480e99a4bb3046e0565113d9dca294e0895d3b0c
workflow graph group-isoforms-batch.cwl

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

https://github.com/Barski-lab/workflows.git

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: 812b0ff40dda18ab7a9a872ff13a577be8531ba6
workflow graph tRNA_selection.cwl

https://github.com/EBI-Metagenomics/ebi-metagenomics-cwl.git

Path: tools/tRNA_selection.cwl

Branch/Commit ID: 583307878ab83c5845c897f03db920ae8e1929e2
workflow graph assm_assm_blastn_wnode

https://github.com/ncbi/pgap.git

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 2353ee2550529ca5b0705c94b32022a21713db18
workflow graph 5S-from-tablehits.cwl

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: tools/5S-from-tablehits.cwl

Branch/Commit ID: b6d3aaf3fa6695061208c6cdca3d7881cc45400d
workflow graph EMG QC workflow, (paired end version). Benchmarking with MG-RAST expt.

https://github.com/proteinswebteam/ebi-metagenomics-cwl.git

Path: workflows/emg-qc-paired.cwl

Branch/Commit ID: 5e8217435bcdd597b2ad236f3e847d13d4c21824
workflow graph scatter-wf4.cwl#main

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: e835bc0487fe42fb330b6222c9be65d18dd81ec9

Packed ID: main
workflow graph wgs alignment and germline variant detection

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/germline_wgs_gvcf.cwl

Branch/Commit ID: b8000c793d6e7ce4d690406c4f914c5c62acd51f
workflow graph RNA-Seq alignment and transcript/gene abundance workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/rnaseq.cwl

Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c